after owning both.. i had a 02 sport and now a 08 v8.. i find the 08 to be much better built and more refined. the 3rd gen v6 with a 4 speed always felt gutless to me, and i never felt like i could tow properly. the new v6 (as we had in our 2 tacomas) is a good option, altho feels like you have to wind it up to get power.. i like the v8s smooth quiet low end power over the v6. both new motors have 5 speeds in them.
the XREAS is awesome for handling and road behavior. and the addition of VVTi to the v8 is great for power, it hauls ass. we can pull 20mpg on the hwy no problem.. only downside is the v8 is full time 4WD, altho i see that as an upside... safer if anything. i also see no issues with the "electronics". my 02 had nearly the same electronics as the 08, except drive by wire... which most new sports cars are drive by wire.. including our IS and all of the new lexus models... i see no problems with it, and actually prefer it now. with "lag" you are as limited as your weakest link, and with a motor, most times the speed to the throttle body opening is not your slowest item to react.
the newer gen is bigger, without being too big. fits great in a small cali garage. the interior is very nice, and the auto climate control is available on all trim levels, not just the limited like the 3rd gen. the 4th gen is built as the lexus GX as well, so some of the nice items transfer over since they are on the same platform.
personally i hated the 4th gens when i had my 3rd gen, but after '06 with the facia changes, i personally think a 4th gen looks nicer.. anyway, a rushed post... but id go 4th gen if you could afford it. and the JBL radio is awesome... we didnt go for NAVI but got the JBL system, ive never been disappointed by the new JBL systems they are putting in... our tacoma had it as well..
the 4th gens are still built in japan also, feels much more rigid and better built than our tacomas (built here in the bay area)